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Un Jan Contreras S, Gardner CM. Environmental fate and behaviour of antibiotic resistance genes and small interference RNAs released from genetically modified crops. J Appl Microbiol 2022; 133:2877-2892. [PMID: 35892194 DOI: 10.1111/jam.15741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 07/21/2022] [Accepted: 07/23/2022] [Indexed: 11/30/2022]
Abstract
Rising global populations have amplified food scarcity across the world and ushered in the development of genetically modified (GM) crops to overcome these challenges. Cultivation of major crops such as corn and soy has favoured GM crops over conventional varieties to meet crop production and resilience needs. Modern GM crops containing small interference RNA molecules and antibiotic resistance genes have become increasingly common in the United States. However, the use of these crops remains controversial due to the uncertainty regarding the unintended release of its genetic material into the environment and possible downstream effects on human and environmental health. DNA or RNA transgenes may be exuded from crop tissues during cultivation or released during plant decomposition and adsorbed by soil. This can contribute to the persistence and bioavailability in soil or water environment and possible uptake by soil microbial communities and further passing of this information to neighbouring bacteria, disrupting microbial ecosystem services such as nutrient cycling and soil fertility. In this review, transgene mechanisms of action, uses in crops, and knowledge regarding their environmental fate and impact to microbes are evaluated. This aims to encapsulate the current knowledge and promote further research regarding unintended effects transgenes may cause.
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Affiliation(s)
- Sandra Un Jan Contreras
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
| | - Courtney M Gardner
- Department of Civil and Environmental Engineering, Washington State University, Pullman, Washington, USA
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Lian F, Yu W, Zhou Q, Gu S, Wang Z, Xing B. Size Matters: Nano-Biochar Triggers Decomposition and Transformation Inhibition of Antibiotic Resistance Genes in Aqueous Environments. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2020; 54:8821-8829. [PMID: 32558563 DOI: 10.1021/acs.est.0c02227] [Citation(s) in RCA: 70] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Antibiotic resistance genes (ARGs) are considered to be a type of emerging contaminant; their interaction with biochar (BC) could affect their dissemination and fate in the environment. Although adsorption of ARGs onto bulk-BC has been reported, the interaction with nanosized BC (nano-BC) is largely unknown. In this study, the interactions of a model extracellular DNA (eDNA, calf thymus DNA) and two typical ARGs (ampC and ermB) extracted from a natural river with bulk- and nano-BCs from two pyrolysis temperatures (400 and 700 °C) were investigated. Only adsorption was observed on bulk-BCs, while not only adsorption but also fragmentation of these eDNA molecules was found to occur on nano-BCs. Also, their replication was greatly inhibited by nano-BCs. The electron paramagnetic resonance results indicated that hydroxyl radicals produced from persistent free radicals (PFRs) on nano-BCs played a major role in the damage of eDNA. Moreover, the direct contact with nonradical reacting sites and PFRs on nano-BCs also contributed to the decay of eDNA. Comparatively, PFRs in bulk-BCs were difficult to be reached by eDNA because of steric hindrance and played a negligible role in destroying eDNA. These findings highlight the importance of the size effect in evaluating the reactivity and related environmental risks of PFRs on BC and improve our understanding on the interaction between ARGs and BC.
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Affiliation(s)
- Fei Lian
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Wenchao Yu
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
| | - Qixing Zhou
- College of Environmental Science and Engineering, Nankai University, Tianjin 300071, China
| | - Shiguo Gu
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Zhenyu Wang
- Institute of Environmental Processes and Pollution Control, and School of Environment and Civil Engineering, Jiangnan University, Wuxi 214122, China
| | - Baoshan Xing
- Stockbridge School of Agriculture, University of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
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Harrison JB, Sunday JM, Rogers SM. Predicting the fate of eDNA in the environment and implications for studying biodiversity. Proc Biol Sci 2019; 286:20191409. [PMID: 31744434 DOI: 10.1098/rspb.2019.1409] [Citation(s) in RCA: 109] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Environmental DNA (eDNA) applications are transforming the standard of characterizing aquatic biodiversity via the presence, location and abundance of DNA collected from environmental samples. As eDNA studies use DNA fragments as a proxy for the presence of organisms, the ecological properties of the complex and dynamic environments from which eDNA is sampled need to be considered for accurate biological interpretation. In this review, we discuss the role that differing environments play on the major processes that eDNA undergoes between organism and collection, including shedding, decay and transport. We focus on a mechanistic understanding of these processes and highlight how decay and transport models are being developed towards more accurate and robust predictions of the fate of eDNA. We conclude with five recommendations for eDNA researchers and practitioners, to advance current best practices, as well as to support a future model of eDNA spatio-temporal persistence.
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Affiliation(s)
- Jori B Harrison
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
| | | | - Sean M Rogers
- Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada
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Sand KK, Jelavić S. Mineral Facilitated Horizontal Gene Transfer: A New Principle for Evolution of Life? Front Microbiol 2018; 9:2217. [PMID: 30319562 PMCID: PMC6167411 DOI: 10.3389/fmicb.2018.02217] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Accepted: 08/30/2018] [Indexed: 11/22/2022] Open
Abstract
A number of studies have highlighted that adsorption to minerals increases DNA longevity in the environment. Such DNA-mineral associations can essentially serve as pools of genes that can be stored across time. Importantly, this DNA is available for incorporation into alien organisms through the process of horizontal gene transfer (HGT). Here we argue that minerals hold an unrecognized potential for successfully transferring genetic material across environments and timescales to distant organisms and hypothesize that this process has significantly influenced the evolution of life. Our hypothesis is illustrated in the context of the evolution of early microbial life and the oxygenation of the Earth's atmosphere and offers an explanation for observed outbursts of evolutionary events caused by HGT.
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Affiliation(s)
- Karina Krarup Sand
- Department of Geography and Earth Sciences, Aberystwyth University, Aberystwyth, United Kingdom
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Stanislav Jelavić
- Nano-Science Center, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
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Högfors-Rönnholm E, Christel S, Dalhem K, Lillhonga T, Engblom S, Österholm P, Dopson M. Chemical and microbiological evaluation of novel chemical treatment methods for acid sulfate soils. THE SCIENCE OF THE TOTAL ENVIRONMENT 2018; 625:39-49. [PMID: 29287211 DOI: 10.1016/j.scitotenv.2017.12.287] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2017] [Revised: 12/21/2017] [Accepted: 12/23/2017] [Indexed: 06/07/2023]
Abstract
Naturally occurring sulfide rich deposits are common along the northern Baltic Sea coast that when exposed to air, release large amounts of acid and metals into receiving water bodies. This causes severe environmental implications for agriculture, forestry, and building of infrastructure. In this study, we investigated the efficiency of ultrafine-grained calcium carbonate and peat (both separately and in combination) to mitigate acid and metal release. The experiments were carried out aerobically that mimicked summer conditions when the groundwater level is low and acid sulfate soils are exposed to oxygen, and anaerobically that is similar to autumn to spring conditions. The ultrafine-grained calcium carbonate dissipated well in the soil and its effect alone and when mixed with peat raised the pH and reduced pyrite dissolution while peat alone was similar to the controls and did not halt metal and acid release. High throughput 16S rRNA gene sequencing identified populations most similar to characterized acidophiles in the control and peat treated incubations while the acidophilic like populations were altered in the calcium carbonate alone and calcium carbonate plus peat treated acid sulfate soils. Coupled with the geochemistry data, it was suggested that the acidophiles were inactivated by the high pH in the presence of calcium carbonate but catalyzed pyrite dissolution in the controls and peat incubations. In conclusion, the anaerobic conditions during winter would likely be sufficient to mitigate acid production and metal release from acid sulfate soils and in the summer, treatment with calcium carbonate was the best mitigation method.
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Affiliation(s)
- Eva Högfors-Rönnholm
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland; Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Stephan Christel
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
| | - Krister Dalhem
- Department of Geology and Mineralogy, Åbo Akademi University, FI-20500 Turku, Finland.
| | - Tom Lillhonga
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Sten Engblom
- Research and Development, Novia University of Applied Sciences, FI-65200 Vaasa, Finland.
| | - Peter Österholm
- Department of Geology and Mineralogy, Åbo Akademi University, FI-20500 Turku, Finland.
| | - Mark Dopson
- Centre for Ecology and Evolution in Microbial Model Systems (EEMiS), Linnaeus University, SE-39231 Kalmar, Sweden.
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Schmidt MP, Martínez CE. Ironing Out Genes in the Environment: An Experimental Study of the DNA-Goethite Interface. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:8525-8532. [PMID: 28732154 DOI: 10.1021/acs.langmuir.7b01911] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
DNA fate in soil plays an important role in the cycling of genetic information in the environment. Adsorption onto mineral surfaces has great impact on this function. This study probes the kinetics, equilibrium behavior and bonding mechanisms associated with adsorption of DNA onto goethite, a common soil mineral. Surface sensitive ATR-FTIR and XPS approaches are applied to directly characterize the DNA-goethite interface. Adsorption kinetics follow a pseudo-first-order model, suggesting adsorption rate is surface limited. Adsorption rate constants increase with DNA concentration, ranging from 3.29 × 10-3 to 3.55 × 10-1 min-1. Equilibrium adsorption, as monitored by ATR-FTIR and XPS, follows the Langmuir model, with a high affinity of DNA for goethite observed (K = 1.25 × 103 and 9.48 × 102 mL/mg for ATR-FTIR and XPS, respectively). ATR-FTIR and XPS characterization of the structure of surface adsorbed DNA demonstrates inner-sphere coordination between backbone phosphate groups of DNA and goethite. Furthermore, adsorbed DNA retains a B-form, suggesting the DNA helix adsorbs on goethite without degradation or alteration to helical structure, despite binding of backbone phosphate groups. This work advances our understanding of the environmental behavior of DNA by characterizing the mechanism of adsorption onto a prominent soil mineral.
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Affiliation(s)
- Michael P Schmidt
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University , Ithaca, New York 14853, United States
| | - Carmen E Martínez
- Soil and Crop Sciences, School of Integrative Plant Science, Cornell University , Ithaca, New York 14853, United States
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Wang Q, Wang W, Wu J, Wang A. Effect of attapulgite contents on release behaviors of a pH sensitive carboxymethyl cellulose-g-poly(acrylic acid)/attapulgite/sodium alginate composite hydrogel bead containing diclofenac. J Appl Polym Sci 2011. [DOI: 10.1002/app.35440] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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